Chuck vs Sarah, Sam, & Lady Valkrie Writer's Cut
by ThereIsAnother
Summary: The Writer's cut of my first story. Takes place after vs. American Hero as Chuck is intersected with a new and more powerful Intersect. Sarah's dealing with her own demons as she goes through hell thinking that she's killed Chuck. They both need each other now more than ever but will they find each other in time? Charah as always.
1. Prologue

**A/N: I have to say I was inspired by BillAtWork's remastered work as of late. Therapy was always one of my favorites and his rework of that has made me want to redo my first story. Hopefully I can improve this story based on what I've learned from writing here on this site.**

**I have to admit when I first did vs. Sam, Sarah, and Lady Valkrie, I really didn't know what I was doing, had no beta, and was just throwing stuff out there as soon as it came out of my head. With that said, this story was and always will be my favorite and that's why I chose to revisit it and do it the "right way" this time.**

**Expect to see hopefully better flow, better grammar, and much more detail within each chapter. I've also added a few new chapters and have added more of the dream link sequences along with much more introspection from the characters especially our girl. I've also taken some of the advice from my original reviewers and have incorporated that in to this story.**

**So while the basis of the story is the same, hopefully you'll find this "Writers cut" a much more enjoyable read and hopefully a more fulfilling one to. My only regret is that passion won't be here to read it but I'm dedicating this story to her, one of the most supportive and biggest Chuck fans out there. **

**So its time to take a walk down memory lane as I welcome the old and the new to the story that will always hold the biggest place in my heart.**

**Thanks to Gladius who will be with me on this journey and for his continued hard work as I throw endless ideas at him.  
**

**Of course I still don't own Chuck or anything in this story but I swear if I had won the Powerball, I'd be owning them soon enough.**

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**Prologue**

**{****Time line: Starts right before vs. American Hero.}**  


The Ring Director walked in to his Los Angeles office. Today could possibly mark the greatest day in the history of his organization. He worked hard and dedicated a majority of his life to the Ring and finally, it would be paying off. After months of disappointments and failed missions, it was finally all coming together. Sure he didn't trust this Shaw guy, but the idiot was so easy to manipulate it wasn't even funny. It didn't take much to convince him to turn against the very government he swore to serve. But pretty much that is how the Ring recruited most of its members. After all, the Government made it easy for people to want to defect. Money, power, and the opportunity to kill without prejudice, yeah, who would not want to join the Ring.

The director walked around his desk and sat in his chair. He had just got back from the underground Intersect facility and the news was positive from the lead scientist. They had informed him that the new Intersect was almost completed and that the Governor Project was moving along as well. The Scientist had asked when the test subject for the Governor would be available and he had informed him it would be just a matter of days. This of course was why he needed to call Agent Shaw. They had titled the new Governor Project code name Eve's Revenge. Sure it was corny, but they needed Shaw at his best and most motivated, why not play to that with the code name? He smiled as he thought of just how pitiful Shaw truly was.

The Director looked over at the clock, knowing that soon would be the time to place possibly one of the most important calls of his life. The set of events that would be put in motion now would almost guarantee him a spot as an Elder. And it all started with the next phone call.

_"This is Daniel Shaw."_

The Director could barely contain his excitement. "Shaw, it is time to initiate project Eve's Revenge. Is everything ready?"

_"Yes sir. The mark has been so easy to manipulate. She actually thinks I care about her. And the love sick moron will do pretty much anything I say."_

The news couldn't have been better as the Director looked out his window over the California skyline. They were so close. "So the Ardenal X20 has been effective against this Agent Walker?" The Director knew this was an experimental drug but his scientist assured him it was ready for field use.

_"Extremely effective. I've been putting small amounts in her coffee for the past few months and she hasn't been able to resist the effects. I could suggest she walks around with a pillowcase over her head and that tramp would do it. I mean the slut is so far gone she even broke down and told me her real name. Can you believe that? How pathetic can you get?"_

Even this surprised the Director. Usually an Agent's real name is something that is never compromised. Especially someone with the secretive past of Sarah Walker. She has more alias' then any agent he had ever seen. But the greatest thing about the fact she told Shaw her real name was a testament to just how affective the Ardenal X20 was. Shaw had told him about how close her and the 'Moron' as Shaw put it, were. The fact that she told Shaw her real name after only a month or so was an indication just how powerful the drug was. "And her feelings for this love sick moron has not caused issues?"

_"In the beginning it was touch and go but lately it has been a lot easier. I believe the Agent you sent did enough to permanently put a rift in their relationship."_

"Good, I'll tell Hannah the good news. Maybe she won't be so pissed knowing that she didn't have a chance to kill the dweeb." The Director paused as he thought about just how happy Hannah will be and what she will be willing to do.. again for him. Yeah, today was going to be a good day and it would be the start of many more to come. He could not control his enthusiasm as he realized how close the Ring was to finishing this major phase of their plan. He still wanted to make sure everything would go on without a hitch though. "You're confident the test subject will follow you into the building?"

_"She'd go through hell and back for me. I'll try to make it as believable as possible, but she'll no doubt come running in after to me. Crying and pleading for me to be with her."_

"Good. The success of this Governor test will be more important than even the Intersect, and Sarah Walker will be vital to that success." The Director stood now as he looked down upon the world he would soon be ruling. "No mistakes Shaw. Make this happen."

_"I understand Sir. I'll not fail you."_

"Yes Daniel, it's time to finally get revenge on those that killed your wife." Oh well, why not add a little encouragement even though he could really care less.

With this, Shaw hung up the phone and gave a slight smile. He had waited a long time to avenge his beloved Eve. He had wanted so badly to just end it quickly when he met the bitch that killed her. Luckily the Director gave him a much sweeter plan. Death would be to quick. He wanted Walker to suffer and what better way to suffer then losing everything you love. Not to mention the enjoyment of using the bitch as a tool would be incentive enough. He couldn't wait to see the pain he would soon be causing to those around her. His smile widened as said bitch came walking through the door from the adjacent room.

"You ready for Burbank, Sam?" asked Shaw as Sarah sat her Luggage next to the bed.

Sarah sighed as she thought about what she would be facing there. "It'll be nice to finally tie up some loose ends." Sarah thought momentarily of the lanky brown - eyed nerd who would be waiting there. A part of her was saddened, but strangely she was also looking forward to finally ending it. She just wanted to move on and be with someone that respected her as the person she was. She did not want to be with someone whose idealistic view of her was that of being a 'real' girl.

Shaw could see she was thinking about the nerd. He patted the bed next to him. He had to get her mind from wandering too much. "Well, I hope you can finally bring closure to this situation with Bartowski. I think it's a waste to keep getting separate rooms." Even though he hated the bitch, he wanted to make her suffer in more ways than one. He would show her just how rough sex could be with him. She would not even know the difference from begging him to beat her, whip her, and do whatever he wanted.

Sarah turned to Shaw, for some strange reason a coldness came over her causing her to shiver. "I hope you understand. I truly enjoy being with you and I love all the time we spend together. But I'm just not ready to take, 'that' step, at least not yet." Sarah hoped he understood.

Shaw could not help but think, _I can't believe I've had to put up with you this long you stupid slut. I should have just let you die from that poison released from the mask. But I knew how important you were to this project. Either way, just one more performance and then you will begin to know what real pain and suffering is. _Shaw didn't even realize he was smirking now as he broke from the musings in his head. "I completely understand. You and Chuck have a history, and I respect you even more for sticking to your guns so to speak." _Yeah I'd like to stick a gun to your face…_

"You're so sweet" replied Sarah as she gently touched the side of Shaw's face. She immediately noticed his flinch at her touch. "You okay?"

Shaw couldn't believe he just flinched. He was better than this and he had to get control. "Yeah, sorry, just your hands were cold." Shaw quickly stood up as the thought of that hand touching his face made him sick inside. "So, you ready to head back to Burbank? We still have some final reports to fill out down at Castle."

Sarah just looked around the room. It seemed so peaceful here… with Daniel. She didn't have to worry about inner walls, or emotions, she could just… well she could just be. Now she would soon have to face the one person that would never let her just be. She let out a deep sigh as she stood to leave. It was time to get this over with and finally move on to a new life. A better life with someone like Shaw.

With that, the two agents left both their rooms and took a cab to the airport. Nothing would ever be the same...

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**A/N: So here we began the journey and what a journey it will be. I look forward to bringing you all along on this ride as hopefully you will get a better glimpse into my thoughts on these chapters as I try to put them to print.**

**A/N2: For vs. The One fans, I already have two chapters in beta so as soon as I get those back, I will be updating that story also.  
**


	2. Chapter 1

**A/N: Now I wanted to remind everyone, this isn't a rewrite of the original. So if you're expecting major character changes or storyline shifts from the original, this will not be happening. With that said, there will be a lot of new stuff and more story line details, but the characters will stay true to what my original intent was.  
**

**This chapter will be a little rough as it sticks very closely to cannon and let me tell you, that is extremely hard to write why these Characters would follow the same awful paths they did in season 3. Hopefully the explanation of the drug explains a little more about Sarah's actions with Shaw as much more detail to her behavior will be revealed as we go on.  
**

**Also, as stated above, this will stay true to the original which means there is a dark patch coming or already here if you consider where cannon was at this point.  
**

**Esardi, I respect you man and I will do my best to give Chuck some balls, but in this story, he was always the more lighthearted, nerdy Chuck that would do anything for Sarah. While the next few chapters will seem like Chuck is getting the short end of the stick, the pay off will come. I've purposefully rethought some chapters because of your review and I will do my best to level it out a little. I always respect your thoughts, so keep ****them coming. **  


**For the Charah shippers out there, the next few chapters will be rough but not in the aspect that they moved on to someone else. I just can't write them moving on, I just won't ever do it. But there will be some dark times coming.  
**

**For everyone else, I appreciate your reviews and if you've ever wanted to know more about a situation in the original or an extended scene here or there, let me know and I will do my best to incorporate it in the story.  
**

**I want to thank my Beta who wasn't here for the original but is now. I know he's a busy man but he still finds the time to help me out. Thanks Gladius.  
**

**And as always, I don't own Chuck or stock in the two by four business.  
**

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**Chapter 1**

**{Back at Castle, Chuck returns from his trip to see Beckman about becoming an official spy}**

Chuck had just arrived back from Washington D.C. where it was finally made official, he was a real spy. Although not quite official until he took his first mission, but still, he was a spy now. He paused in thought as he walked into his empty apartment. Morgan was working late and so that gave him some alone time to reflect on all the things he had been through the past couple months.

He made his way to his room where he dropped his bag on the floor, took off his jacket, and sat on the edge of his bed, staring at his Tron poster. He had a fleeting thought that how different things would've been if he had used his innate ability to plan, on an effective mission plan to win back Sarah. A plan that would have been implemented way before Shaw, Hannah, or any of the recent messes he had managed to get himself in.

He sighed deeply as he rubbed the front of his face thinking back to the time everything could have changed. The time after their mission in the suburbs. If only he would have done things differently, what would his life be like now he thought.

He took a deep breath, letting out not only the oxygen from his lungs, but the bygones that were weighing him down. It wasn't time to sulk, it was time to take action. Whether he wished things could be different or not, he felt the undeniable urge to get off his butt and make something happen. Sarah was a complicated girl and he needed to uncomplicate things for her. It all started with the fact he was a spy. That would have to finally break down that barrier that she had always claimed was between them.

Chuck was convinced now was the time as he stood to go to the bathroom to freshen up. After, he would head over to Castle and finally, finally confront the one he loved. As he made his way into the bathroom, a strange feeling overcame him like things were about to change, forever.

**{* * *}**

Chuck made it to Castle in relatively good time considering the traffic. He was both excited and nervous about talking to Sarah but he couldn't delay any longer. Chuck knew now was the time to confront Sarah.

As he bounded down the steps, and came around to the conference room, he noticed Shaw was out of the room and he was never more grateful that it would be just him and Sarah. He took a calming breath as he gained the courage that would be needed for what lay ahead.

**. . .**

"I'm going to Washington, okay, and I'm going with Shaw." Sarah would not even look at him as she just shuffled through some folders on the table. Obviously there was no method to her madness, she just did not want to concentrate on Chuck. It took all her will power to at least give the impression that she was organizing folders.

Chuck was in complete shock. Sarah wasn't even giving him a chance to explain. It was like she had just shut down.

"Wait a minute. Wasn't this the plan? There's nothing stopping us from being together now. I passed my spy test." Chuck tried to reach for her hand but quickly retracted when he saw the anger in her eyes when she finally looked at him.

Sarah couldn't believe how ignorant he was.

"That's why I can't be with you, okay. You're not...you're not the same guy I fell for." At least she was able to look him in the eyes as she broke his heart. She owed him at least that considering she had not dared look at him when the conversation started.

Chuck just shook his head. He was a smart guy, always able to process information at an incredible rate. Unfortunately now, none of the information was making much sense. "How am I not the same guy?"

Sarah slammed down the folder she was holding in her hand. "You killed somebody. Chuck! I saw you kill the mole!" What is wrong with him is he really that stupid that he cannot figure this out on his own? She angrily thought to herself.

Chuck took a deep breath. He had to calm down because the way Sarah was acting was completely irrational, it made absolutely no sense at all, almost as if she wasn't the same person he always knew.

"Sarah, I know what you think you saw, but it's not that simple, it's more complicated than that. It's not what you think and I need you to believe me." This time Chuck reached out a hand to at least connect with her on some level. His touch always seemed to at least calm her. Unfortunately, this time it seemed to have the adverse effect.

Sarah violently ripped her arm away from him.

"Well I don't believe you Chuck. You're so good at lying now I doubt you even know the difference. I'll never be able to trust you… Ever!" Sarah could not bear to look at him anymore. He was a lying bastard and she despised him for what he did to her. Lou, Jill, Hannah, Prague, every one of those horrible thoughts blasted through her, increasing tenfold the anger she held inside. She was willing to give up her life for him and he just spat in her face and screwed around with anything with two legs and dark hair. She had enough. She was not about to take another minute of this abuse.

Chuck felt his insides turn over as he saw the hurt and anger in Sarah's eyes. "Sarah, please. Please you have to know I did this all for you."

Sarah misheard the 'I did this all _for_ you' and thought he had said 'I did this all _because of_ you'' The full force of her anger inside was suddenly released like the hoover Dam collapsing in on itself.

"Shut up! Shut up now!" screamed Sarah. She was seconds from ripping out her knife and shoving it through his cold dark heart.

Chuck took a step back. Never before had he seen Sarah so enraged. He couldn't understand why she was reacting like this. This was not like her. Never before had he seen such a reaction. Sure he'd seen her mad, but Sarah was always in control, always the cool head in the most dire circumstances. Matter of fact, he had never remembered a time where she had ever yelled at him, at least not in anger like this. Now, all that was gone, and it scared him.

Sarah was beyond fuming, she just wanted the idiot to stop accusing her of everything. Stop blaming her for turning such an innocent, loving, truthful man into a cold hearted spy, just like her. Chuck was supposed to be her way out of this life, he was the one that was supposed to save her. Instead, he just turned his back on her and that pissed her off more.

"I know. I know I made you do everything. I know I changed you, it's all my fault. I'm an emotionless killer!**" **Sarah was trying her best to calm down, she knew she had to gain some semblance of control. This was not like her at all but and plus, she didn't want to worry Daniel who was in the other room. "But hey, that's what makes me a great spy, right?"

Chuck shook his head as his heart started to break. He wanted so bad to hold her, to go back to how it was before. He didn't care about anything else, he just wanted the old Sarah back. He desperately wanted things back the way they were before Prague.

"Sarah, please. That is not what I meant. You're everything to me and I never felt like you made me…"

Sarah slapped him hard across the face. "Chuck, so help me God. If you don't shut up and leave, I'll kill you myself." Sarah knew she was looking at Chuck, but all she could think about was what Daniel had been telling her over the past weeks. 'Chuck is a spy because of her.' 'She trained him so well.' 'Chuck would not be here if it weren't for her.' 'Chuck will be better off because of all she has done to help him become a spy.' All these words just kept repeating over and over in her head. She didn't even realize she had slapped him until she noticed the look of astonishment along with the bright red mark on his face.

Chuck couldn't believe what just happened. He felt as if he were in a horrible nightmare and he couldn't get out. Nothing made sense and he couldn't figure out how things went so wrong. His intention was to come here and win Sarah back but if anything, he had completely pushed her away. It was like Sarah wasn't even listening to a word he said. In a strange way, it felt to Chuck as if she was possessed by a demon or something.

Sarah stood there, beginning to shake with anger as the only thoughts in her head were those put there by Shaw. She heard nothing of what Chuck was actually trying to say, only the continued promptings and urgings of Daniel.

Chuck knew he had to do something. He just could not let this go on. This was not the Sarah he knew and he would not leave her like this. He had to share with her his true feelings and do it in a way where there could be no doubt. Chuck cautiously lifted his hands to her face.

"Sarah, I Lo…" Chuck never finished as Sarah punched him in the side of the mouth. She hit him so hard it felt as if his wisdom tooth had been knocked down his throat. Chuck took the punch straight on as his eyes started watering.

"What the hell Sarah?" asked Chuck as he tasted the blood coming from the corner of his mouth. Now he was the one getting angry. That punch was the last straw and this time, it was Chuck's turn to snap.

"Look Sarah, I don't know what the hell has gotten into you but enough is enough. I've had to take a back seat; literally, almost since the day we first met. I've done everything you've asked of me and you still don't want me. You cling to any spy with man parts, but the man who has always been there for you, the man who would do anything for you, you treat him like a piece of shit." It was this last statement that Chuck noticed must of struck a chord.

Sarah felt a pain in her heart as the words of Chuck hit home. She still remembered how Daniel had taught her to control her emotions. He had told her great spies do not feel emotion. Daniel had given her such wonderful advice lately; what would she do without him? To think this imbecile in front of her at one time actually meant something to her. His beautiful brown eyes, the way he always made her laugh, his curly brown hair. _What the hell am I thinking?_ Sarah shook her head trying to clear her thoughts from the war going on between her heart and her brain.

Chuck noticed something happening with Sarah and continued his assault now.

"Sarah you got all pissed when I wouldn't leave with you in Prague. I get it, that sucked but you have to see the bigger picture. What would have happened if we took that path in our lives? Huh? What life would we've had, always being on the run? How happy would that have made you?" Chuck was right up in her face now. He was not about to back down.

"Then I come back to apologize, realizing I was wrong, and you treat me like crap. The situation in Prague was a major setback yes, but your solution was going and practicing your seduction skills on some drug lord. And to top it all off, you drill into my brain that we can never be together because I'm just an asset all along knowing the only way to become a spy is taking a red test. So what was I supposed to do Sarah?"

Chuck was through. "You know what? You never did care about me did you? You just wanted an excuse to get out of the spy life and I was the most convenient schnook you could play your little con on." Chuck would never forgive himself for what he said next. "I mean you are the best con person out there, right. I just can't believe I fell for it."

It was then Sarah realized something very out of the ordinary was taking place within her. Why had she not been listening to Chuck, why were all these other thoughts in her head. _Why the heck am I relying so much on Daniel?_ She was not mad, but something just did not feel right. It was then that Shaw walked in, a very large cup of coffee in his hand.

Seeing the super spy walk in, Chuck knew it was time to get out of there before he vomited his dinner everywhere. It was bad enough dealing with Sarah but now with this prick here, he couldn't take it. Without another word, he stormed out of Castle.

"Chuck, wait!" pleaded Sarah, but Chuck was up the stairs and out the door before he could hear her say, "I'm… sorry…"

**{* * *}**

**{Back at Ellie's Apartment}  
**

"You don't stop, you don't quit, you never go to far." Ellie could see the pain in her Brother's eyes. She had seen something very similar back when Jill destroyed him but this was much worse. She had to do something because she could not stand to see her little brother broken yet again. Especially since the one doing, the breaking was nothing like Jill.

Chuck realized that although maybe he wasn't so much at blame for the way things happened between he and Sarah, he sure as hell needed to decide how much it was worth fighting for. How much was he willing to sacrifice to make Sarah happy again? What he saw down at Castle hours earlier was not the Sarah he knew. Maybe he was to blame, maybe it was all his fault. Whatever the case, he loved Sarah too much to put her through this kind of emotional breakdown. He had to do something… he had to do more.

Ellie's words inspired him as he gave her a quick hug and kiss and then was out the door. It might not be the right thing to do but he was heading back to Castle, he could not let things end between him and Sarah at least not the way they had just done. He had to make this right.

**. . .**

Chuck looked in the rear view mirror as he was close to arriving at Castle. What surprised him was that he did not recognize the person staring back.

"Man, what have I become?" Chuck asked out loud as if maybe some hidden force could provide clarity. He couldn't help but think back over his life the past 3½ years.

His stomach turned as he thought how easy lying was to him now. How manipulating his family and friends was second nature to him. How he actually enjoyed fighting, and more importantly, the thrill of beating the snot out of people. What sickened him the most was how he has treated the women in his life, not just Sarah. Bryce Larkin had nothing on him in the egotistical chauvinistic category. How could it be so easy for him to sleep with one person while really being in love with someone else? What a bastard he was for doing that to not only Jill, but Hannah and most importantly Sarah. It was at that moment he realized he truly was not Chuck Bartowski anymore.

The person who he really was, the person who was raised by the most incredible sister the world would ever know, the person that never lied, always put family first, always cared about how others felt, that person was gone. In its place was nothing but a cold hearted spy. The very thing he swore for over two years he never wanted to become.

He looked down towards the picture of Sarah that he still kept near the speedometer in his nerd herder.

"Sarah, you're right. I'm not the same guy, and even though some things have made me better, as a whole I'm a horrible person for what I've done. I don't want to live like this anymore, I want to make it right. I promise, I will be the old Chuck again."

As if gaining strength from his confession, Chuck hit the gas as he sped to Castle, not wanting to waste another minute. He was going to do whatever it took to get Sarah back and nothing was going to stop him.

**. . .**

When Chuck walked into Castle, he noticed right away Shaw and Sarah kissing. The horrific sight felt twenty times worse than a punch to the gut, or even the recent punch to the face by the very woman he saw now in the embrace of another. All his strength, his will power, his last vestige of hope, it all seemed to deflate like a balloon losing all its air. It was crushing to see something that he wanted so bad, and here, the living two by four was in the spot that should be his. What he wanted to do to Shaw at that exact moment would have made even Casey proud. But then the moment in the car came flooding back to him. This was not who he was. This was not who he wanted to be. He was better than this and he was determined that the old Chuck would always come through.

He knew that it was over now and Sarah's heart was taken. If he was honest with himself, he had the shot, unfortunately he missed wildly. He would wait though, but not interfere, after all, there really was only one Sarah. The last thing he wanted was Sarah getting even more upset than she already was. He promised himself right then and there that he would always be there for her, but never force her to do anything she didn't want to. He knew at that moment that he loved her with every fiber of his being, and because of that love, he was not going to force her to choose. He was not going to cause more conflict for her. Why? Because that is what the real Chuck would do.

Chuck was so caught up in his own thoughts that he never noticed the two spies break their kiss. It startled him a little when Shaw walked past Chuck, placing a strong hand on his shoulder.

"Take care of her." Then he was gone, Chuck never noticed the smirk spread across his face as he walked out of sight of Chuck and Sarah..

Chuck, seeing Shaw gone, cautiously approached Sarah. He knew he had to tread carefully and he really just wanted to be there for her. He could tell something was upsetting her yet once again. He just hoped him being here wasn't the cause this time.

"Sarah, I'm not going to say anything else except that I'm sorry and if there is anything I can do to help, I will."

Sarah paused for a split second as she heard the thoughtfulness in Chuck's voice. She turned to him and could see the sincerity in his eyes. For a brief moment, the feelings before Prague over took her. But it was only for a moment.

"Shaw is going to the ring headquarters as bait and I am not going to let him go alone." Sarah regained her composure as she ran the software that would track Shaw's beacon.

Chuck had a decision to make. A part of him would love for Shaw to get blown up into a million slivers of wood, and taken out of the picture, but the real Chuck new what he had to do. Walking over to the Castle computer, he brought up the Castle defenses and activated Detention Mode in the room where Sarah was busy working on the tracking software.

Sarah realizing what happened immediately turned and yelled at Chuck, as the security wall came down.

"What are you doing? I just knew you would pull something like this!" She reached for her gun but remembered she left it in the armory for cleaning. How could she be so stupid she thought as she banged her fist against the glass wall.

Chuck was heartbroken that Sarah's first thought was that he was trying to somehow win her back by omission. Could he blame her though? Wasn't he just thinking like that earlier. Sure when push comes to shove he would never do that, but he wasn't completely free of fault here. This is what he had become in Sarah's eyes and could he really blame her? The disappointment in those blue orbs pained him more than anything. He would give up everything just so that sparkle would be back in those eyes.

"He's not going in alone, I am going in with him and I'm not coming back without him." He placed a nervous hand on the window where her fist was. "I promise you Sarah."

Sarah wanted to cry, her original anger crumbling like the Berlin wall, "But why would you do this?" This wasn't how the new Chuck acted, this was how her old Chuck would have acted. But Shaw said…

"Because I know how much he means to you". At this Chuck turned around and left Castle, not seeing Sarah as she leaned her saddened face against the glass.

Sarah was in complete shock. So much in her head was trying to tell her it was just a ploy so Chuck could kill Shaw, but unlike the past two months, it was her heart that was winning this battle. No matter what the crazy thoughts were going on in her head, she was still a spy and her partners were in danger. Relationships aside, she had a job to do. She swore somehow, some way she was going to get Chuck back, she quickly corrected herself, she would get both her partners back.

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**A/N: I know, rough chapter. I always hated that the two didn't have it out more in that conversation. They were both to blame for what had happened but I always thought, at that moment, Sarah was way to unreasonable with Chuck. Also the fact I never wanted to shoot Shaw more than I did when he walked in to interrupt them. My heart broke for Chuck at that moment in the show. **


	3. Chapter 2

**A/N: ****This is the setup chapter. This is where you need to pay attention to whats happening because this chapter is the basis for things to come. ****  
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**I don't own Chuck.  
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**Chapter 2**

With some unconventional help from Jeff and Lester, that could rival the NSA's best surveillance techniques, Chuck finally found where Shaw had been taken. Realizing how dangerous this could be and not wanting Jeff and Lester further involved, Chuck did his best to convince the two morons to leave. After some borderline sadistic compromises, the two left, excited about the prospects of what Chuck promised them.

Chuck was still shaking his head trying to figure out how to get out of this mess when he approached what looked to be a long ago abandoned warehouse. Chuck knew better then to trust the simple appearance of the abandoned facility, of course it helped that the Intersect verified to him what lay beneath. Searching around one more time to make sure the coast was clear of prying eyes, Chuck quickly put on his assault gear, making sure his tranq pistols were loaded, and headed into the warehouse.

He figured at the most he was about 10 minutes behind Shaw so he knew now would be a good time as any to make his move. He was sure the Ring would not be expecting something so soon especially with all the precaution they took to keep Shaw's where about hidden.

As soon as he entered the warehouse, Chuck scanned the room looking for any sign of a trap. He listened for voices and still nothing. He cautiously continued into the warehouse, pistols raised in front of him as he swept the room for any sign of life. Chuck stood perplexed as all he saw was a strange soda machine on the far wall of the warehouse.

Double checking to make sure the current level was secure, he walked up to the soda machine, realizing that it wasn't even the more popular brands of soda, when all of a sudden he felt a flash coming on. He wasn't prepared to flash on a soda machine but the images he saw and the code he was able to decipher from the flash gave him what he needed as he walked up to the machine and pressed the sequence of codes. He wondered briefly how in the world the Intersect would have such a code and why it wouldn't be changed by now. No matter though, the code worked and Chuck was on his way down, checking his front pocket to make sure that General Beckman's locator device was securely stashed there.

**{* * *}**

* * *

"Director, we have a situation." One of the guards in the underground lab alerted the Director to an intruder that was detected just moments earlier.

The Director just stood there, smug as can be. Of course he was expecting this as he nonchalantly looked over his shoulder at the guard. "So, what's the problem?"

The guard nervously replied, "We have a CIA agent in the building."

Now the director was just annoyed. Had the guard not been part of the numerous debriefings they had about what this new objective would entail? There was one thing the Director could not stand and that was incompetence. Matter of fact, he made a mental note to arrange a little accident for the guard once this mission was over. "I know there is a CIA Agent in the building, you idiot. It's our test subject." The Director just shook his head in disgust. "Now be a good little soldier and follow the plan to lead her down to the lab."

The guard became even more nervous. It was obvious this news was not going to be taken very well. "Uh, no sir, this is a male CIA agent. Agent Charles Carmichael."

The director was completely caught off guard. Luckily his face was turned from the guard otherwise he would have witnessed complete shock. How could this happen the Director fumed? That damn Shaw assured them Agent Walker would be the one to come. He was going to make sure someone paid for this.

He stalked over to the area where Shaw was loading up the hand held device that would deliver the newly developed Governor.

"Shaw!" The venom was evident in the Director's voice.

Shaw almost dropped the device as he heard the Director shout his name. "Yes, Director?" Shaw turned cautiously to see a not so pleasant look on the Director's face. He could tell the Director was beyond pissed.

The Director had a finger pointed directly at Shaw's face. "You assured me Agent Walker would be here."

Shaw just shook his head, not understanding what was going on. He knew the silent alarm had already gone off so what the hell was going on? "Yeah, she should be here now, I saw the silent alarm flash so I assumed it was her." A sudden ill feeling started growing in the pit of his stomach as he stared beyond the Director to the two doors leading into the underground lab.

The Director was practically spitting out the next words. "You idiot, it's Agent Carmichael, and he's ALONE damn it!" Yeah someone was going to pay for this.

A panicked look spread across Shaw's face. "What in the world is that idiot thinking?" Shaw could not believe Bartowski was coming down here and to what, to save him? What kind of fool was he? Shaw knew he had played the part just right and there was no way any other man would have just given up the fight. Didn't the moron know that by saving him, it would just mean Sarah and he would be together? Shaw shuddered, thinking to himself what kind of man would pick the feelings of a useless woman over his own? Shaw just shook his head in confusion.

The Director did not get to his position because he was lucky. Although lately he was definitely more on edge than usual, he still was one of the smartest and brightest, albeit ruthless, men in the entire Ring organization. So just when most would have given up on the plan, the Director suddenly came up with a plan of his own. He quickly pulled himself together, putting aside his need to punish Shaw for now. He had to think clearly otherwise everything he had worked so hard for could come crashing down. No, he would not let that happen. Matter of fact, this could actually prove to be a huge advantage.

With an air of confidence, relative to his position in the Ring, the Director smirked as he looked towards Shaw. "Just a minor setback Shaw." The Director's mood suddenly did a complete turnaround. "Do we have the 'special' intersect upload setup and the audio package ready to go?'

Shaw suddenly gained understanding at what the Director was getting at. He could not help but feel a sense of admiration realizing he had chosen the right organization to be part of. "Everything is ready to go. We just need to switch over the software to run the alternate program instead of the main upload."

The Director rubbed his hands together as a wicked grin spread across his face. "Gooood. I want you to set up this 'special' surprise for our new guest. We'll just move our plan in a different direction and deal with Agent Walker at a later time. Who knows, having Agent Carmichael on our side ahead of schedule may actually pay dividends." Yeah, this could turn out to be a blessing in disguise. Two Human Intersects working for the Ring, oh yeah, this might just be a day to remember for the rest of his life.

**{* * *}**

* * *

Chuck had made it to the bottom floor and was just turning a corner when he ran right into a group of Ring Agents, who apparently were not at all surprised to see him. He had to act quickly as he called upon the Intersect to give him the skills he would need to take them all out. Once the flash was complete, he just smiled at the group.

"This is really going to hurt guys." Then with a quickness born out of months of training, and desperation to save a fellow agent, even if it was Shaw, Chuck quickly proceeded to take out the three men in no time at all.

Even Chuck was impressed at the skills the Intersect could provide sometimes as he looked down upon the three unconscious agents surrounding him. However, his self-admiration was brief as he knew he had to find Shaw and get the hell out of the facility. Taking one final look at the fallen men, he quickly proceeded down the hall.

It didn't take Chuck long and he found what he was looking for, or at least what the Intersect instructed him he was looking for. There was a set of large white doors now directly in front of him. There was no being cautious now. He knew Shaw was on the other side and no matter how he felt about the jerk, he had to do this. He had do this for Sarah but also because in the end, it was who he really was. Never would Chuck Bartowski ever leave a man behind. This conviction was what gave him the courage to face whoever was on the other side of those doors, holding Shaw hostage.

Without further thought, he reached forward and grabbed a hold of both handles , swinging the doors wide open in one fell swoop, making sure to bring up both his guns again. What he saw almost made him drop those very guns.

Shaw knew he had to get a hold of the situation quickly but he also knew what a tool Bartowski was. Almost as easy to manipulate as Walker but without the heavy doses of Ardenal. "Chuck, I don't want you to freak out. I know you're going to freak out but you have to listen to me." Shaw was trying everything to hide his grin. Oh this was going to be so much fun. Not that it mattered, he hated the blonde whore anyway, but to think he actually had to drug that wench just to get her to acknowledge him... and all for this worthless weakling in front of him? Well it was time to start collecting on a long overdue debt.

Chuck was completely taken back by what he saw in the room and it wasn't that Shaw was standing there in front of him, arms opened wide. Chuck had always had a knack for situational awareness. It's what made him so good at video games. Well, being a spy was sometimes just like one big video game and Chuck was now quickly processing the layout of his newest tournament map.

Chuck noticed at the far end of the room, it looked very similar to a miniaturized version of the Intersect 2.0 room, with a hand recognition device podium sprouting up right in the dead center. To the right of this enormous room was what must have been some kind of laboratory that looked like something out of a Frankenstein movie. It was complete with jars of various colored liquids, vials of blood, monitoring devices, and electronic wiring everywhere. He also noticed that there were numerous I.V. bags, and even a couple gurneys with arm and leg straps. Chuck wondered if the Emperor had used something very similar in his transformation of Anakin to Darth Vader. His musing quickly vanished as he refocused on the whole reason he was here. Standing in the middle of everything was the bane of his existence, his new nemesis, his rival. "Shaw? Shaw what are you doing? And why are you not being tortured or bound in some way?" Not that Chuck would have been happy to see that in any way.

Shaw could see the confusion on Chuck's face as he glanced quickly to his right making sure the device was ready for activation. "Chuck, the Ring is not who or what you think they are. You have been deceived from the beginning by the CIA and NSA." There is the hook, let us see if he takes the bait Shaw mused quietly.

Even in his wonderment at the many facets of the room he now stood in, Chuck was taken aback by what he heard come out of Shaw's mouth. "What the heck are you talking about Shaw?" Chuck raised his tranq gun in the direction of Shaw. The mere mention of the Ring filling Chuck with anger. The Ring had taken everything from him, everything. And now Shaw was trying to talk to him as if they were the good guys?

Shaw tensed a little bit seeing the tranq gun raised towards him. He had to be convincing enough to get Chuck to turn and being unconscious would not help that situation. "Listen to me Chuck. I was sent to help you and get you safely away from the rogue Government agency that is manipulating you." Shaw tried putting on his determined trustworthy look.

Chuck was not having any of this as he quickly scanned the room once again, this time taking in the occupants and not just the equipment. There were about ten people in the room, but a majority looked like scientists and doctors. The 'Darth Vader Room' had two men standing in front of what now Chuck recognized as plutonium grade canisters near the electronic equipment behind the gurneys. He saw the high res monitors in the room and tried to focus on the information on the screen but Shaw started moving back into the Intersect area which brought his attention back to the double agent.

"What are you doing here Shaw and what exactly is this place?" Chuck needed some answers and he needed them now. The more time went by, the more anxious Chuck was getting to know the truth.

Shaw raised his hands almost in a surrendering type motion. "Chuck, just calm down. I assure you we're not the enemy. And to prove it, there's something I want you to see." He had to contain his laughter as he was about to give Chuck a very special surprise.

Before Chuck could do or say anything, everyone but him quickly put on dark glasses and the room in front of him lit up with a multitude of images. By the time he realized what was happening, the imbedded images already started flashing across the screens, locking his eyes in the open position and flooding his brain with the new upload. The problem as Chuck quickly learned was this was not the normal Intersect pictures he was used to seeing uploaded into his brain. No, these were much worse. These images were of... "Sarah?"

Chuck stood still as he was transfixed by the images of all the missions Agent Walker had ever been on since her induction into the CIA. However, instead of the countless acts of heroism, or the many honorable sacrifices Agent Walker had made throughout her career, these images were of the darkest times. Some images were so impulsive that it almost made Chuck throw up. They were deplorable to look upon as Chuck tried everything to turn away but of course, he could not. He had to stand there and absorb all the images of Agent Walker stabbing and cutting people up in horrible acts of violence. The images showed her shooting people in cold blood apparently for no reason other than they got in the way of her objective. Chuck saw her poisoning people, beating helpless victims, torturing captives by ammonia injection, and all kinds of sickening things. However, these images were not ones that made Chuck feel like throwing up. These horrible acts of needless violence and torture were not the images that shattered Chuck's heart.

It was the next set of images that destroyed Chuck. The images of all Agent Walker's seduction missions displayed on the screens now in high-resolution detail. Surveillance images of Bryce and her, Lon Kirk, Cole, and even Shaw. The most private of moments between Agent Walker and her marks displayed unforgettably on the screens in front of Chuck. The physical pain could not compare to the pain in his heart as Chuck lowered his head, the screens suddenly going dark.

Shaw couldn't be happier seeing the broken form of the sorry excuse for an Intersect before him. This would be one of his greatest victories. "You see Chuck, Agent Walker has used you from the beginning." Shaw was very careful not to use Sarah's first name. He needed Chuck to separate Sarah from the Agent. Shaw then pressed a button on the remote control he now held in his hand. It was then the sound system crackled to life as the room filled with numerous conversations between Sarah and her superiors.

"No, it can't be." Chuck tried to cover his ears as the conversations were coming across crystal clear in hi res fiber optic enhanced sound. He heard Agent Walker talking about how Chuck was an easy mark she could manipulate, 'piece of cake' he heard her say. Then he heard her say she would kill him if he tried to run. Chuck didn't know these conversations were taken completely out of context, spliced together by the high tech Ring analysts. All he knew was the pain he was feeling from hearing them being played loud and clear over the sound system. It might as well of been fingernails against a chalkboard for the way it made him feel.

Chuck fell to his knees, placing his hands behind his lowered head as he held himself in a crash position. He literally felt like his heart had exploded. He just could not believe Agent Walker had betrayed him from the beginning. It was at this time he began retreating into the darkest recesses of his soul. His body was reacting to a wound that had opened in his heart and could never be fixed. Jill was but a bump in the road compared to what he was going through now. All Chuck could do in his broken state was repeat the words, "Why..., why…"

Shaw was smiling as he looked over to the Director who had a strange look on his face. Well a stranger than usual look. Either way, nothing would deter from his crowning achievement of finally, breaking the Intersect once and for all. The specially designed Emotion Altering Intersect was working like a charm. It was so easy to splice out the pictures of the real agents on the screen and replace them with Walker's image. It was quite genius if he did say so himself, and it was working wonders as he smiled looking over at the crumbled form of the imbecile. Now the emotionless wreck of a human being would be his to control and manipulate any way he saw fit. His smile grew even larger seeing the pain and suffering the idiot was going through.

"Chuck, I tried everything to help you along the way. Yes, I know you didn't kill the mole and that Casey did. I didn't say anything because the loyalty you showed your former partner in the face of losing the one you loved was incredible. I knew you could be a true hero and while times were not always pleasant, you grew from my training. Agent Walker just held you back as she and her agency wanted to keep you for themselves to manipulate you and use you how they saw fit. I mean come on Chuck, how many times did Agent Walker lie to you or mislead you? 'Trust me' can only hold so much water when not followed by action." Wow, even he was impressed with his own little speech. Yeah the broken down piece of shit was his.

Chuck was close to completely giving in to the darkness. He had never felt this kind of soul piercing coldness before. Even after Stanford, he had never felt the tearing of his soul like this. He was teetering on the edge, all it would take is a slight nudge, and the darkness would completely consume him. He was broken mind, body, and spirit and he could not function, didn't want to function anymore. For what seemed like a recurring theme in his life, although not to this extent, Chuck was once again giving up.

Shaw cautiously moved toward Chuck. "You see Chuck; the Ring needs your help. We just need your help to bring these unpatriotic rogue Agents to justice. You're too good a person to let people like Sarah… Agent Walker destroy this country." Damn it Shaw thought, that was close.

That name... Sarah, Chuck thought. The darkness was all around him, controlling him, engulfing him, inviting him to its cold dark core, but that name... Sarah, was not associated with this evil Agent Walker, the one that had done such horrible things. In the face of his greatest moment of need, it was then Chuck heard his Sisters soft loving voice' _you don't stop, you don't quit!' _But Ellie, it was all a lie, Chuck cried to himself. He tried to plead with subconscious Ellie that Sarah was not the person that she knew. She was not the same person that they had grown to love. It was then, in his darkest hour, Chuck suddenly had flashes, not Intersect flashes, but flashes that felt like they were coming from his heart, not his brain.

Sarah walking into the Buy More, the words that he rapped playing through his mind, "Vicky Vale, Vick, Vicky Vale". Then he flashed on Sarah hugging his Sister on so many occasions, displaying such a sisterly bond. Sarah coming into the Buy More, always looking so beautiful. But then the images of Sarah with Bryce flashed intersect style. Then Sarah and Cole, and the worst, Sarah and Shaw. But those flashes were quickly over powered by the special moments with just he and Sarah. Chuck was starting to come out of the darkness as his own subconscious was helping him by causing his original Intersect to reboot, and override the one just put in. The Intersect flashes were always mechanical by nature, but these seemed to reflect his heart as they completely overrode what was just put in. For every Bryce/Sarah, there was Sarah holding his hand. For every Sarah/Shaw, there was Sarah eating a hamburger or sizzling shrimp with him.

Shaw didn't even recognize the change happening to Chuck. His pride had taken over and so he continued his verbal assault. "So you see Chuck, we need you to help bring justice to Agent Walker. We need you to help us terminate Agent Walker."

That was all it took as Chuck Jumped to his feet, in the blink of an eye, aiming one of his tranq guns straight at Shaw. The darkness completely gone now as realization hit him. He secretly initiated the tracking device that was now in his hand.

Shaw was completely taken by surprise as he froze dead in his tracks. In all his arrogance, he definitely did not expect this. The Ring doctors had specifically confirmed to him that the 'Sarah Intersect' would completely destroy Chuck's emotions. It would block any part of his brain that held the good memories between Sarah and Chuck.

Chuck could see the shock on Shaw's face. Honestly, after what had just happened, Chuck was a little surprised he was able to come out of it too. Maybe his dad was right all those years ago, always saying how special he was. "You made a very big mistake Shaw. You assumed I was a spy. You assumed the Intersect you downloaded into me was stronger than the one I have, and the truth I know in my heart. I'll never be like you or these Ring agents. I'll never be a cold hearted ruthless, emotionless killer." Chuck paused as his thoughts went to Sarah. "You want to know who I am. You want to know who I truly am?" Chuck was so angry now but not because of what happened to him. He was mortified at what Shaw did and was doing to Sarah. This pond scum was using Sarah like a piece of garbage, and it was going to end now.

Chuck looked deep into Shaw's eyes, a determination never before felt in his entire life. "I'm Sarah's Chuck. Always have been" Chuck slowly squeezed the trigger on his tranq gun.

Chucked jumped as a gun shot rang out from behind him. He definitely was not expecting that as he quickly turned around to see the Director standing there with a smoking gun. "Wow, you're a bad shot, sir." Chuck remarked as he raised his other gun aiming at the Director, assuming the shot was meant for him.

"Chuck, why?" Shaw yelled as he crumbled to the ground, his hand holding the open wound to his chest.

Chuck quickly turned back to Shaw who he now saw crumbled in a heap on the floor, blood pouring from where his hand covered the hole in his chest. Chuck felt like he was in a twilight zone movie. He looked back to the Director as he stood frozen in place, not quite understanding what exactly just happened, or more importantly, why.

The director just shrugged his shoulders like it was no big deal. Judging by the unconcerned looks of everyone else in the room, this must have been normal behavior for the director of the Ring. "I can't stand failure." Replied the director as he holstered his gun and started moving towards the door. "Make sure this one dies a horrible death" as he pointed at Chuck, realizing their plan had failed. With that, the director quickly left.

The guards came rushing forward, each with guns raised as they ordered Chuck to drop his weapon.

Chuck could never understand why people did this. Even in the face of everything that had just happened, Chuck was still a nerd at heart. He and Morgan had both had long discussions about people that were captured in movies and the captures were told to kill them. It always was delayed somehow for some ridiculous reason. Like right now, why were they even worried about him dropping his gun? Why didn't they just shoot? Their loss, Chuck thought as he instantly flashed.

Images of close contact judo and defensive stances flashed in his mind as the Intersect calculated everything he would need to take out the guards surrounding him. "Sorry guys but this is really going... oh never mind."

It was over in seconds as Chuck took out three of the four guards instantly. He ducked the fourths attempt to shoot him as a stray bullet just flew over his head. This gave Chuck the chance he needed as he round house kicked the guard knocking him out instantly.

Chuck quickly scanned the room as more guards came in to subdue him, once again, why not just shoot? Wow his nerd musings sure had strange timings he laughed to himself. It was then he saw the radiation alarm going off in the Laboratory section of the room. "Oh Shit...toki mushrooms." Chuck knew this was not good.

One of the doctors, who had a definite look of horror on his face was suddenly frantically screaming at those left in the room. "We have got to get out of here, major contaminant breach."

The warning was just a little too late as a small explosion rocked the entire room, emanating from the Darth Vader laboratory. It was a small explosion, but still was able to rock the entire floor causing debris to fly everywhere.

Chuck barely had time to react as a small shiny fragment flew through the air towards his head. He felt a powerful jolt as if someone punched him in the side of the head, and then a warm liquid sensation coming from his temple. He started getting dizzy as he fell to one knee.

Everything started going hazy as Chuck was quickly losing consciousness. He completely forgot about the guards, about Shaw, the Director, everything was just a haze as he heard gun shots from the opening of the door. He went down to both knees, his head feeling like it had gained an extra twenty pounds. He could not look up as he felt soft tender hands trying to lift him.

"Chuck, we have to get out of here," said a frantic familiar voice.

Wow, that voice was like an angel Chuck thought as the fog of dizziness clouded his vision.

"Chuck, where is Shaw?" Sarah was trying to get Chuck to focus but it was no use. She quickly scanned the room where she saw Shaw lying on the floor just inside the intersect section of the room. She gently let go of Chuck as he was wavering on his knees. "I'll be right back." she assured Chuck as she went to go check on Shaw.

Sarah quickly ran over to where Shaw lay sprawled out in a pool of blood. She fell to her knees as she lifted his head gingerly. She checked for a pulse even though it didn't look good with all the blood. Luckily, she felt a pulse, it was weak, but it still meant Shaw was alive. "Shaw you have to wake up. We have to get out of here." Sarah was pleading with Shaw as tears started flowing from her eyes.

In the blink of an eye, Shaw's hand darted to Sarah's chest where a sharp pain hit her right near her heart muscle. "What the hell?" yelled Sarah as she grabbed her chest, where a slight pain was emanating. She felt as if somehow Shaw had just shocked her.

Shaw was barely hanging on as he looked into Sarah's eyes. He may have lost this battle, but he was going to make sure that this war would always remember him. "It was Chuck, he… he… shot… me…" It was Shaw's last act of despicable cowardice as he left the world of the living to join his brethren in hell.

Sarah did not register everything at first. A strange pain still affecting her chest, not to mention the small explosions happening around her, she would have to mourn another day. She was still an agent in the CIA and she needed to get the Intersect to safety. She would process everything later as she quickly got up to go get Agent Carmichael. She never noticed the used remnants of the Governor Test device in Shaw's cold dead hand.

Just before reaching Chuck, she noticed what looked to be a recording device near the laboratory. Thinking this might come in handy, she ran over to pick it up and then ran back to get Chuck.

Chuck and Sarah barely made it out of the building as the Bomber dropped the Bunker Buster and within seconds, the whole place exploded.

Chuck was bleeding slightly from his head wound, and consciousness was getting more and more difficult to hang on to. It felt like someone lit a match inside his temporal lobe and the pulsing was causing the worst headache he ever felt. It felt as if his mind was on fire.

Sarah quickly pulled out her phone but noticed that the signal was all wacky. She looked around for anything that would cause interference but nothing she could see. Before she could even think, Ellie's phone number was suddenly dialed on Sarah's phone and she never even touched it.

"Sarah, I think we should call Ellie. I don't feel very well." Then Chuck collapsed.

Sarah tried to ask him one very important question as she waited for Ellie to pick up, still trying to figure out how the phone did that. However, something Shaw said still bothered her. She did not want to wait as she held Chuck's head in her lap. "What happened in there Chuck?"

* * *

**A/N: Hopefully for those that read the first story, this chapter contained a lot more detail of what was going on. After I originally wrote this chapter, the episode of Chuck came out where it revealed Volkhoff was actually who he was because of the Intersect. That is what I originally wanted it to come across as but I don't think I succeeded the first go around. Hopefully this time I did.**

**I know these are some tough chapters but it will be getting better soon. Big thank you to all those reading this and I'd love to hear your thoughts.**


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